Encoding biological sequences into Voss representation

BioVossEncoder

A Julia package for encoding biological sequences into Voss representation

Installation

BioVossEncoder is a   Julia Language   package. To install BioVossEncoder, please open Julia's interactive session (known as REPL) and press ] key in the REPL to use the package mode, then type the following command

pkg> add BioVossEncoder

Encoding BioSequences

This package provides a simple and fast way to encode biological sequences into Voss representation. The main struct provided by this package is BinarySequenceMatrix which is a wrapper of BitMatrix that encodes a biological sequence into a binary matrix. The following example shows how to encode a DNA sequence into a binary matrix.

julia> using BioSequences, BioVossEncoder

julia> seq = dna"ACGT"

julia> BinarySequenceMatrix(seq)

BinarySequenceMatrix{NucleicAcidAlphabet, BitMatrix}(DNAAlphabet{4}(), Bool[1 0 0 0; 0 1 0 0; 0 0 1 0; 0 0 0 1])

For simplicity the BinarySequenceMatrix struct provides a property bsm that returns the BitMatrix representation of the sequence.

julia> BinarySequenceMatrix(seq).bsm

4×4 BitMatrix:
 1  0  0  0
 0  1  0  0
 0  0  1  0
 0  0  0  1

Similarly another function that makes use of the BinarySequenceMatrix struct is binary_sequence_matrix which returns the BitMatrix representation of a sequence directly.

julia> binary_sequence_matrix(seq)

4×4 BitMatrix:
 1  0  0  0
 0  1  0  0
 0  0  1  0
 0  0  0  1